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Subject: Re: [OMPI users] Multiple mpiexec's within a job (schedule within a scheduled machinefile/job allocation)
From: Adams, Brian M (briadam_at_[hidden])
Date: 2009-07-30 18:36:09


I found the manual pages for mpirun and orte_hosts, which have a pretty thorough description of these features. Let me know if there's anything else I should check out.

My quick impression is that this will meet at least 90% of user needs out of the box as most (all?) users will run with number of job processors that divides into PPN or is a multiple of PPN.

The docs imply that the relative indexing is relative to nodes as opposed to slots. If so, it's easy to cover my cases 1 and 2 with modulo arithmetic right on the command line, but the edge case 3 might require creation of host files or a maps file, specifying specific nodes and slots. I'm still trying to fully wrap my head around the way the scheduling works and the nodes/slots distinction, so have to think on this. For example, in a PBS/Torque environment, I guess each processor gets an entry as a "node" in the $PBS_NODEFILE, so maybe this won't be an issue for many of our machines.

Another potential gotcha is the scheduler driving my M scheduler processes ideally runs asynchronously (since not all compute jobs take equal time as parameters vary), so initially jobs 0--M could be on resource blocks 0--M in order, but if job 2 finishes first, I'd want to put job M+1 on block 2. So I might end up needing some glue code anyway for the dynamic scheduling case. What's in ORTE today will likely work great in the static scheduling case.

Brian

________________________________
From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Ralph Castain
Sent: Thursday, July 30, 2009 2:08 PM
To: Open MPI Users
Subject: Re: [OMPI users] Multiple mpiexec's within a job (schedule within a scheduled machinefile/job allocation)

Let me know how it goes, if you don't mind. It would be nice to know if we actually met your needs, or if a tweak might help make it easier.

Thanks
Ralph

On Jul 30, 2009, at 1:36 PM, Adams, Brian M wrote:

Thanks Ralph, I wasn't aware of the relative indexing or sequential mapper capabilities. I will check those out and report back if I still have a feature request. -- Brian

________________________________
From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Ralph Castain
Sent: Thursday, July 30, 2009 12:26 PM
To: Open MPI Users
Subject: Re: [OMPI users] Multiple mpiexec's within a job (schedule within a scheduled machinefile/job allocation)

On Jul 30, 2009, at 11:49 AM, Adams, Brian M wrote:

Apologies if I'm being confusing; I'm probably trying to get at atypical use cases. M and N need not correspond to the number of nodes/ppn nor ppn/nodes available. By node vs. slot doesn't much matter, as long as in the end I don't oversubscribe any node. By slot might be good for efficiency in some apps, but I can't make a general case for it.

I think what you proposed offers some help in the case where N is an integer multiple of the number of available nodes, but perhaps not in other cases. I must be missing something here, so instead of being fully general, perhaps consider a specific case. Suppose we have 4 nodes, 8 ppn (32 slots is I think the ompi language). I might want to schedule, for example

1. M=2 simultaneous N=16 processor jobs: Here I believe what you suggested will work since N is a multiple of the available number of nodes. I could use either npernode 4 or just bynode and I think get the same result: an even distribution of tasks. (similar applies to, e.g., 8x4, 4x8)

Yes, agreed

2. M=16 simultaneous N=2 processor jobs: it seems if I use bynode or npernode, I would end up with 16 processes on each of the first two nodes (similar applies to, e.g., 32x1 or 10x3). Scheduling many small jobs is a common problem for us.

3. M=3 simultaneous, N=10 processor jobs: I think we'd end up with this distribution (where A-D are nodes and 0-2 jobs)

A 0 0 0 1 1 1 2 2 2
B 0 0 0 1 1 1 2 2 2
C 0 0 1 1 2 2
D 0 0 1 1 2 2

where A and B are over-subscribed and there are more than the two unused slots I'd expect in the whole allocation.

Again, I can manage all these via a script that partitions the machine files, just wondering which scenarios OpenMPI can manage.

Have you looked at the relative indexing in 1.3.3? You could specify any of these in relative index terms, and have one "hostfile" that would support 16x2 operations. This would work then for any allocation.

Your launch script could even just do it, something like this:

mpirun -n 2 -host +n0:1,+n1:1 app
mpirun -n 2 -host +n0:2,+n1:2 app

etc. Obviously, you could compute the relative indexing and just stick it in as required.

Likewise, you could use the new "seq" (sequential) mapper to achieve any desired layout, again utilizing relative indexing to avoid having to create a special hostfile for each run.

Note that in all cases, you can specify a -n N that will tell OMPI to only execute N processes, regardless of what is in the sequential mapper file or -host.

If none of those work well, please let me know. I'm happy to create the required capability as I'm sure LANL will use it too (know of several similar cases here, but the current options seem okay for them).

Thanks!
Brian

-----Original Message-----
From: users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>
[mailto:users-bounces_at_[hidden]] On Behalf Of Ralph Castain
Sent: Wednesday, July 29, 2009 4:19 PM
To: Open MPI Users
Subject: Re: [OMPI users] Multiple mpiexec's within a job
(schedule within a scheduled machinefile/job allocation)

Oh my - that does take me back a long way! :-)

Do you need these processes to be mapped byslot (i.e., do you
care if the process ranks are sharing nodes)? If not, why not
add "-bynode" to your cmd line?

Alternatively, given the mapping you want, just do

mpirun -npernode 1 application.exe

This would launch one copy on each of your N nodes. So if you
fork M times, you'll wind up with the exact pattern you
wanted. And, as each one exits, you could immediately launch
a replacement without worrying about oversubscription.

Does that help?
Ralph

PS. we dropped that "persistent" operation - caused way too
many problems with cleanup and other things. :-)

On Jul 29, 2009, at 3:46 PM, Adams, Brian M wrote:

Hi Ralph (all),

I'm resurrecting this 2006 thread for a status check. The
new 1.3.x
machinefile behavior is great (thanks!) -- I can use
machinefiles to
manage multiple simultaneous mpiruns within a single torque
allocation (where the hosts are a subset of $PBS_NODEFILE).
However, this requires some careful management of machinefiles.

I'm curious if OpenMPI now directly supports the behavior I need,
described in general in the quote below. Specifically,
given a single
PBS/Torque allocation of M*N processors, I will run a
serial program
that will fork M times. Each of the M forked processes
calls 'mpirun -np N application.exe' and blocks until completion.
This seems akin to the case you described of "mpiruns executed in
separate windows/prompts."

What I'd like to see is the M processes "tiled" across the
available
slots, so all M*N processors are used. What I see instead
appears at
face value to be the first N resources being oversubscribed M times.

Also, when one of the forked processes returns, I'd like to
be able to
spawn another and have its mpirun schedule on the resources
freed by
the previous one that exited. Is any of this possible?

I tried starting an orted (1.3.3, roughly as you suggested
below), but
got this error:

orted --daemonize
[gy8:25871] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file
runtime/orte_init.c at line 125

----------------------------------------------------------------------
---- It looks like orte_init failed for some reason; your parallel
process is likely to abort. There are many reasons that a parallel
process can fail during orte_init; some of which are due to
configuration or environment problems. This failure
appears to be an
internal failure; here's some additional information (which
may only
be relevant to an Open MPI developer):

orte_ess_base_select failed
--> Returned value Not found (-13) instead of ORTE_SUCCESS

----------------------------------------------------------------------
---- [gy8:25871] [[INVALID],INVALID] ORTE_ERROR_LOG: Not
found in file
orted/orted_main.c at line 323

I spared the debugging info as I'm not even sure this is a correct
invocation...

Thanks for any suggestions you can offer!
Brian
----------
Brian M. Adams, PhD (briadam_at_[hidden]<mailto:briadam_at_[hidden]>) Optimization and
Uncertainty
Quantification Sandia National Laboratories, Albuquerque, NM
http://www.sandia.gov/~briadam

From: Ralph Castain (rhc_at_[hidden])
Date: 2006-12-12 00:46:59

Hi Chris

Some of this is doable with today's code....and one of these
behaviors is not. :-(

Open MPI/OpenRTE can be run in "persistent" mode - this allows
multiple jobs to share the same allocation. This works much as you
describe (syntax is slightly different, of
course!) - the first mpirun will map using whatever mode was
requested, then the next mpirun will map starting from where the
first one left off.

I *believe* you can run each mpirun in the background.
However, I don't know if this has really been tested enough to
support such a claim. All testing that I know about to-date has
executed mpirun in the foreground - thus, your example
would execute
sequentially instead of in parallel.

I know people have tested multiple mpirun's operating in parallel
within a single allocation (i.e., persistent mode) where
the mpiruns
are executed in separate windows/prompts.
So I suspect you could do something like you describe -
just haven't
personally verified it.

Where we definitely differ is that Open MPI/RTE will *not* block
until resources are freed up from the prior mpiruns.
Instead, we will attempt to execute each mpirun immediately - and
will error out the one(s) that try to execute without sufficient
resources. I imagine we could provide the kind of "flow
control" you
describe, but I'm not sure when that might happen.

I am (in my copious free time...haha) working on an "orteboot"
program that will startup a virtual machine to make the persistent
mode of operation a little easier. For now, though, you
can do it by:

1. starting up the "server" using the following command:
orted --seed --persistent --scope public [--universe foo]

2. do your mpirun commands. They will automagically find
the "server"
and connect to it. If you specified a universe name when
starting the
server, then you must specify the same universe name on
your mpirun
commands.

When you are done, you will have to (unfortunately)
manually "kill"
the server and remove its session directory. I have a
program called
"ortehalt"
in the trunk that will do this cleanly for you, but it
isn't yet in
the release distributions. You are welcome to use it,
though, if you
are working with the trunk - I can't promise it is
bulletproof yet,
but it seems to be working.

Ralph

On 12/11/06 8:07 PM, "Maestas, Christopher Daniel"
<cdmaest_at_[hidden]>
wrote:

Hello,

Sometimes we have users that like to do from within a single job
(think schedule within an job scheduler allocation):
"mpiexec -n X myprog"
"mpiexec -n Y myprog2"
Does mpiexec within Open MPI keep track of the node list it
is using
if it binds to a particular scheduler?
For example with 4 nodes (2ppn SMP):
"mpiexec -n 2 myprog"
"mpiexec -n 2 myprog2"
"mpiexec -n 1 myprog3"
And assume this is by-slot allocation we would have the following
allocation:
node1 - processor1 - myprog
- processor2 - myprog
node2 - processor1 - myprog2
- processor2 - myprog2
And for a by-node allocation:
node1 - processor1 - myprog
- processor2 - myprog2
node2 - processor1 - myprog
- processor2 - myprog2

I think this is possible using ssh cause it shouldn't
really matter
how many times it spawns, but with something like torque it
would get
restricted to a max process launch of 4. We would want the third
mpiexec to block processes and eventually be run on the first
available node allocation that frees up from myprog or
myprog2 ....

For example for torque, we had to add the following to
osc mpiexec:

---
Finally, since only one mpiexec can be the master at a
time, if your
code setup requires that mpiexec exit to get a result, you
can start a
"dummy"
mpiexec first in your batch
job:
mpiexec -server
It runs no tasks itself but handles the connections of
other transient
mpiexec clients.
It will shut down cleanly when the batch job exits or you
may kill the
server explicitly.
If the server is killed with SIGTERM (or HUP or INT), it
will exit
with a status of zero if there were no clients connected at
the time.
If there were still clients using the server, the server
will kill all
their tasks, disconnect from the clients, and exit with status 1.
---
So a user ran:
mpiexec -server
mpiexec -n 2 myprog
mpiexec -n 2 myprog2
And the server kept track of the allocation ... I would
think that the
orted could do this?
Sorry if this sounds confusing ... But I'm sure it will
clear up with
any further responses I make. :-) -cdm
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