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Subject: Re: [OMPI users] SLURM environment variables at runtime
From: Henderson, Brent (brent.henderson_at_[hidden])
Date: 2011-02-24 10:55:43


I'm running OpenMPI v1.4.3 and slurm v2.2.1. I built both with the default configuration except setting the prefix. The tests were run on the exact same nodes (I only have two).

When I run the test you outline below, I am still missing a bunch of env variables with OpenMPI. I ran the extra test of using HP-MPI and they are all present as with the srun invocation. I don't know if this is my slurm setup or not, but I find this really weird. If anyone knows the magic to make the fix that Ralph is referring to, I'd appreciate a pointer.

My guess was that there is a subtle way that the launch differs between the two products. But, since it works for Jeff, maybe there really is a slurm option that I need to compile in or set to make this work the way I want. It is not as simple as HP-MPI moving the environment variables itself as some of the numbers will change per process created on the remote nodes.

Thanks,

Brent

[brent_at_node2 mpi]$ salloc -N 2
salloc: Granted job allocation 29
[brent_at_node2 mpi]$ srun env | egrep ^SLURM_ | head
SLURM_NODELIST=node[1-2]
SLURM_NNODES=2
SLURM_JOBID=29
SLURM_TASKS_PER_NODE=1(x2)
SLURM_JOB_ID=29
SLURM_NODELIST=node[1-2]
SLURM_NNODES=2
SLURM_JOBID=29
SLURM_TASKS_PER_NODE=1(x2)
SLURM_JOB_ID=29
[brent_at_node2 mpi]$ srun env | egrep ^SLURM_ | wc -l
66
[brent_at_node2 mpi]$ srun env | egrep ^SLURM_ | sort > srun.out
[brent_at_node2 mpi]$ which mpirun
~/bin/openmpi143/bin/mpirun
[brent_at_node2 mpi]$ mpirun -np 2 --bynode env | egrep ^SLURM_ | head
SLURM_NODELIST=node[1-2]
SLURM_NNODES=2
SLURM_JOBID=29
SLURM_TASKS_PER_NODE=8(x2)
SLURM_JOB_ID=29
SLURM_SUBMIT_DIR=/mnt/node1/home/brent/src/mpi
SLURM_JOB_NODELIST=node[1-2]
SLURM_JOB_CPUS_PER_NODE=8(x2)
SLURM_JOB_NUM_NODES=2
SLURM_NODELIST=node[1-2]
[brent_at_node2 mpi]$ which mpirun
~/bin/openmpi143/bin/mpirun
[brent_at_node2 mpi]$ mpirun -np 2 --bynode env | egrep ^SLURM_ | wc -l
42 <-- note, not 66 as above!
[brent_at_node2 mpi]$ mpirun -np 2 --bynode env | egrep ^SLURM_ | sort > mpirun.out
[brent_at_node2 mpi]$ diff srun.out mpirun.out
2d1
< SLURM_CHECKPOINT_IMAGE_DIR=/mnt/node1/home/brent/src/mpi
4,5d2
< SLURM_CPUS_ON_NODE=8
< SLURM_CPUS_PER_TASK=1
8d4
< SLURM_DISTRIBUTION=cyclic
10d5
< SLURM_GTIDS=1
22,23d16
< SLURM_LAUNCH_NODE_IPADDR=10.0.205.134
< SLURM_LOCALID=0
25c18
< SLURM_NNODES=2

---
> SLURM_NNODES=1
28d20
< SLURM_NODEID=1
31,35c23,24
< SLURM_NPROCS=2
< SLURM_NPROCS=2
< SLURM_NTASKS=2
< SLURM_NTASKS=2
< SLURM_PRIO_PROCESS=0
---
> SLURM_NPROCS=1
> SLURM_NTASKS=1
38d26
< SLURM_PROCID=1
40,56c28,35
< SLURM_SRUN_COMM_HOST=10.0.205.134
< SLURM_SRUN_COMM_PORT=43247
< SLURM_SRUN_COMM_PORT=43247
< SLURM_STEP_ID=2
< SLURM_STEP_ID=2
< SLURM_STEPID=2
< SLURM_STEPID=2
< SLURM_STEP_LAUNCHER_PORT=43247
< SLURM_STEP_LAUNCHER_PORT=43247
< SLURM_STEP_NODELIST=node[1-2]
< SLURM_STEP_NODELIST=node[1-2]
< SLURM_STEP_NUM_NODES=2
< SLURM_STEP_NUM_NODES=2
< SLURM_STEP_NUM_TASKS=2
< SLURM_STEP_NUM_TASKS=2
< SLURM_STEP_TASKS_PER_NODE=1(x2)
< SLURM_STEP_TASKS_PER_NODE=1(x2)
---
> SLURM_SRUN_COMM_PORT=45154
> SLURM_STEP_ID=5
> SLURM_STEPID=5
> SLURM_STEP_LAUNCHER_PORT=45154
> SLURM_STEP_NODELIST=node1
> SLURM_STEP_NUM_NODES=1
> SLURM_STEP_NUM_TASKS=1
> SLURM_STEP_TASKS_PER_NODE=1
59,62c38,40
< SLURM_TASK_PID=1381
< SLURM_TASK_PID=2288
< SLURM_TASKS_PER_NODE=1(x2)
< SLURM_TASKS_PER_NODE=1(x2)
---
> SLURM_TASK_PID=1429
> SLURM_TASKS_PER_NODE=1
> SLURM_TASKS_PER_NODE=8(x2)
64,65d41
< SLURM_TOPOLOGY_ADDR=node2
< SLURM_TOPOLOGY_ADDR_PATTERN=node
[brent_at_node2 mpi]$
[brent_at_node2 mpi]$
[brent_at_node2 mpi]$
[brent_at_node2 mpi]$
[brent_at_node2 mpi]$ /opt/hpmpi/bin/mpirun -srun -n 2 -N 2 env | egrep ^SLURM_ | sort > hpmpi.out
[brent_at_node2 mpi]$ diff srun.out hpmpi.out
20a21,22
> SLURM_KILL_BAD_EXIT=1
> SLURM_KILL_BAD_EXIT=1
41,48c43,50
< SLURM_SRUN_COMM_PORT=43247
< SLURM_SRUN_COMM_PORT=43247
< SLURM_STEP_ID=2
< SLURM_STEP_ID=2
< SLURM_STEPID=2
< SLURM_STEPID=2
< SLURM_STEP_LAUNCHER_PORT=43247
< SLURM_STEP_LAUNCHER_PORT=43247
---
> SLURM_SRUN_COMM_PORT=33347
> SLURM_SRUN_COMM_PORT=33347
> SLURM_STEP_ID=8
> SLURM_STEP_ID=8
> SLURM_STEPID=8
> SLURM_STEPID=8
> SLURM_STEP_LAUNCHER_PORT=33347
> SLURM_STEP_LAUNCHER_PORT=33347
59,60c61,62
< SLURM_TASK_PID=1381
< SLURM_TASK_PID=2288
---
> SLURM_TASK_PID=1592
> SLURM_TASK_PID=2590
[brent_at_node2 mpi]$
[brent_at_node2 mpi]$
[brent_at_node2 mpi]$ grep SLURM_PROCID srun.out
SLURM_PROCID=0
SLURM_PROCID=1
[brent_at_node2 mpi]$ grep SLURM_PROCID mpirun.out
SLURM_PROCID=0
[brent_at_node2 mpi]$ grep SLURM_PROCID hpmpi.out
SLURM_PROCID=0
SLURM_PROCID=1
[brent_at_node2 mpi]$
> -----Original Message-----
> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On
> Behalf Of Jeff Squyres
> Sent: Thursday, February 24, 2011 9:31 AM
> To: Open MPI Users
> Subject: Re: [OMPI users] SLURM environment variables at runtime
>
> The weird thing is that when running his test, he saw different results
> with HP MPI vs. Open MPI.
>
> What his test didn't say was whether those were the same exact nodes or
> not.  It would be good to repeat my experiment with the same exact
> nodes (e.g., inside one SLURM salloc job, or use the -w param to
> specify the same nodes for salloc for OMPI and srun for HP MPI).
>
>
> On Feb 24, 2011, at 10:02 AM, Ralph Castain wrote:
>
> > Like I said, this isn't an OMPI problem. You have your slurm
> configured to pass certain envars to the remote nodes, and Brent
> doesn't. It truly is just that simple.
> >
> > I've seen this before with other slurm installations. Which envars
> get set on the backend is configurable, that's all.
> >
> > Has nothing to do with OMPI.
> >
> >
> > On Thu, Feb 24, 2011 at 7:18 AM, Jeff Squyres <jsquyres_at_[hidden]>
> wrote:
> > I'm afraid I don't see the problem.  Let's get 4 nodes from slurm:
> >
> > $ salloc -N 4
> >
> > Now let's run env and see what SLURM_ env variables we see:
> >
> > $ srun env | egrep ^SLURM_ | head
> > SLURM_JOB_ID=95523
> > SLURM_JOB_NUM_NODES=4
> > SLURM_JOB_NODELIST=svbu-mpi[001-004]
> > SLURM_JOB_CPUS_PER_NODE=4(x4)
> > SLURM_JOBID=95523
> > SLURM_NNODES=4
> > SLURM_NODELIST=svbu-mpi[001-004]
> > SLURM_TASKS_PER_NODE=1(x4)
> > SLURM_PRIO_PROCESS=0
> > SLURM_UMASK=0002
> > $ srun env | egrep ^SLURM_ | wc -l
> > 144
> >
> > Good -- there's 144 of them.  Let's save them to a file for
> comparison, later.
> >
> > $ srun env | egrep ^SLURM_ | sort > srun.out
> >
> > Now let's repeat the process with mpirun.  Note that mpirun defaults
> to running one process per core (vs. srun's default of running one per
> node).  So let's tone mpirun down to use one process per node and look
> for the SLURM_ env variables.
> >
> > $ mpirun -np 4 --bynode env | egrep ^SLURM_ | head
> > SLURM_JOB_ID=95523
> > SLURM_JOB_NUM_NODES=4
> > SLURM_JOB_NODELIST=svbu-mpi[001-004]
> > SLURM_JOB_ID=95523
> > SLURM_JOB_NUM_NODES=4
> > SLURM_JOB_CPUS_PER_NODE=4(x4)
> > SLURM_JOBID=95523
> > SLURM_NNODES=4
> > SLURM_NODELIST=svbu-mpi[001-004]
> > SLURM_TASKS_PER_NODE=1(x4)
> > $ mpirun -np 4 --bynode env | egrep ^SLURM_ | wc -l
> > 144
> >
> > Good -- we also got 144.  Save them to a file.
> >
> > $ mpirun -np 4 --bynode env | egrep ^SLURM_ | sort > mpirun.out
> >
> > Now let's compare what we got from srun and from mpirun:
> >
> > $ diff srun.out mpirun.out
> > 93,108c93,108
> > < SLURM_SRUN_COMM_PORT=33571
> > < SLURM_SRUN_COMM_PORT=33571
> > < SLURM_SRUN_COMM_PORT=33571
> > < SLURM_SRUN_COMM_PORT=33571
> > < SLURM_STEP_ID=15
> > < SLURM_STEP_ID=15
> > < SLURM_STEP_ID=15
> > < SLURM_STEP_ID=15
> > < SLURM_STEPID=15
> > < SLURM_STEPID=15
> > < SLURM_STEPID=15
> > < SLURM_STEPID=15
> > < SLURM_STEP_LAUNCHER_PORT=33571
> > < SLURM_STEP_LAUNCHER_PORT=33571
> > < SLURM_STEP_LAUNCHER_PORT=33571
> > < SLURM_STEP_LAUNCHER_PORT=33571
> > ---
> > > SLURM_SRUN_COMM_PORT=54184
> > > SLURM_SRUN_COMM_PORT=54184
> > > SLURM_SRUN_COMM_PORT=54184
> > > SLURM_SRUN_COMM_PORT=54184
> > > SLURM_STEP_ID=18
> > > SLURM_STEP_ID=18
> > > SLURM_STEP_ID=18
> > > SLURM_STEP_ID=18
> > > SLURM_STEPID=18
> > > SLURM_STEPID=18
> > > SLURM_STEPID=18
> > > SLURM_STEPID=18
> > > SLURM_STEP_LAUNCHER_PORT=54184
> > > SLURM_STEP_LAUNCHER_PORT=54184
> > > SLURM_STEP_LAUNCHER_PORT=54184
> > > SLURM_STEP_LAUNCHER_PORT=54184
> > 125,128c125,128
> > < SLURM_TASK_PID=3899
> > < SLURM_TASK_PID=3907
> > < SLURM_TASK_PID=3908
> > < SLURM_TASK_PID=3997
> > ---
> > > SLURM_TASK_PID=3924
> > > SLURM_TASK_PID=3933
> > > SLURM_TASK_PID=3934
> > > SLURM_TASK_PID=4039
> > $
> >
> > They're identical except for per-step values (ports, PIDs, etc.) --
> these differences are expected.
> >
> > What version of OMPI are you running?  What happens if you repeat
> this experiment?
> >
> > I would find it very strange if Open MPI's mpirun is filtering some
> SLURM env variables to some processes and not to all -- your output
> shows disparate output between the different processes.  That's just
> plain weird.
> >
> >
> >
> > On Feb 23, 2011, at 12:05 PM, Henderson, Brent wrote:
> >
> > > SLURM seems to be doing this in the case of a regular srun:
> > >
> > > [brent_at_node1 mpi]$ srun -N 2 -n 4 env | egrep
> SLURM_NODEID\|SLURM_PROCID\|SLURM_LOCALID | sort
> > > SLURM_LOCALID=0
> > > SLURM_LOCALID=0
> > > SLURM_LOCALID=1
> > > SLURM_LOCALID=1
> > > SLURM_NODEID=0
> > > SLURM_NODEID=0
> > > SLURM_NODEID=1
> > > SLURM_NODEID=1
> > > SLURM_PROCID=0
> > > SLURM_PROCID=1
> > > SLURM_PROCID=2
> > > SLURM_PROCID=3
> > > [brent_at_node1 mpi]$
> > >
> > > Since srun is not supported currently by OpenMPI, I have to use
> salloc - right?  In this case, it is up to OpenMPI to interpret the
> SLURM environment variables it sees in the one process that is launched
> and 'do the right thing' - whatever that means in this case.  How does
> OpenMPI start the processes on the remote nodes under the covers?  (use
> srun, generate a hostfile and launch as you would outside SLURM, ...)
> This may be the difference between HP-MPI and OpenMPI.
> > >
> > > Thanks,
> > >
> > > Brent
> > >
> > >
> > > From: users-bounces_at_[hidden] [mailto:users-bounces_at_open-
> mpi.org] On Behalf Of Ralph Castain
> > > Sent: Wednesday, February 23, 2011 10:07 AM
> > > To: Open MPI Users
> > > Subject: Re: [OMPI users] SLURM environment variables at runtime
> > >
> > > Resource managers generally frown on the idea of any program
> passing RM-managed envars from one node to another, and this is
> certainly true of slurm. The reason is that the RM reserves those
> values for its own use when managing remote nodes. For example, if you
> got an allocation and then used mpirun to launch a job across only a
> portion of that allocation, and then ran another mpirun instance in
> parallel on the remainder of the nodes, the slurm envars for those two
> mpirun instances -need- to be quite different. Having mpirun forward
> the values it sees would cause the system to become very confused.
> > >
> > > We learned the hard way never to cross that line :-(
> > >
> > > You have two options:
> > >
> > > (a) you could get your sys admin to configure slurm correctly to
> provide your desired envars on the remote nodes. This is the
> recommended (by slurm and other RMs) way of getting what you requested.
> It is a simple configuration option - if he needs help, he should
> contact the slurm mailing list
> > >
> > > (b) you can ask mpirun to do so, at your own risk. Specify each
> parameter with a "-x FOO" argument. See "man mpirun" for details. Keep
> an eye out for aberrant behavior.
> > >
> > > Ralph
> > >
> > >
> > > On Wed, Feb 23, 2011 at 8:38 AM, Henderson, Brent
> <brent.henderson_at_[hidden]> wrote:
> > > Hi Everyone, I have an OpenMPI/SLURM specific question,
> > >
> > > I'm using MPI as a launcher for another application I'm working on
> and it is dependent on the SLURM environment variables making their way
> into the a.out's environment.  This works as I need if I use HP-
> MPI/PMPI, but when I use OpenMPI, it appears that not all are set as I
> would like across all of the ranks.
> > >
> > > I have example output below from a simple a.out that just writes
> out the environment that it sees to a file whose name is based on the
> node name and rank number.  Note that with OpenMPI, that things like
> SLURM_NNODES and SLURM_TASKS_PER_NODE are not set the same for ranks on
> the different nodes and things like SLURM_LOCALID are just missing
> entirely.
> > >
> > > So the question is, should the environment variables on the remote
> nodes (from the perspective of where the job is launched) have the full
> set of SLURM environment variables as seen on the launching node?
> > >
> > > Thanks,
> > >
> > > Brent Henderson
> > >
> > > [brent_at_node2 mpi]$ rm node*
> > > [brent_at_node2 mpi]$ mkdir openmpi hpmpi
> > > [brent_at_node2 mpi]$ salloc -N 2 -n 4 mpirun ./printenv.openmpi
> > > salloc: Granted job allocation 23
> > > Hello world! I'm 3 of 4 on node1
> > > Hello world! I'm 2 of 4 on node1
> > > Hello world! I'm 1 of 4 on node2
> > > Hello world! I'm 0 of 4 on node2
> > > salloc: Relinquishing job allocation 23
> > > [brent_at_node2 mpi]$ mv node* openmpi/
> > > [brent_at_node2 mpi]$ egrep
> 'NODEID|NNODES|LOCALID|NODELIST|NPROCS|PROCID|TASKS_PER'
> openmpi/node1.3.of.4
> > > SLURM_JOB_NODELIST=node[1-2]
> > > SLURM_NNODES=1
> > > SLURM_NODELIST=node[1-2]
> > > SLURM_TASKS_PER_NODE=1
> > > SLURM_NPROCS=1
> > > SLURM_STEP_NODELIST=node1
> > > SLURM_STEP_TASKS_PER_NODE=1
> > > SLURM_NODEID=0
> > > SLURM_PROCID=0
> > > SLURM_LOCALID=0
> > > [brent_at_node2 mpi]$ egrep
> 'NODEID|NNODES|LOCALID|NODELIST|NPROCS|PROCID|TASKS_PER'
> openmpi/node2.1.of.4
> > > SLURM_JOB_NODELIST=node[1-2]
> > > SLURM_NNODES=2
> > > SLURM_NODELIST=node[1-2]
> > > SLURM_TASKS_PER_NODE=2(x2)
> > > SLURM_NPROCS=4
> > > [brent_at_node2 mpi]$
> > >
> > >
> > > [brent_at_node2 mpi]$ /opt/hpmpi/bin/mpirun -srun -N 2 -n 4
> ./printenv.hpmpi
> > > Hello world! I'm 2 of 4 on node2
> > > Hello world! I'm 3 of 4 on node2
> > > Hello world! I'm 0 of 4 on node1
> > > Hello world! I'm 1 of 4 on node1
> > > [brent_at_node2 mpi]$ mv node* hpmpi/
> > > [brent_at_node2 mpi]$ egrep
> 'NODEID|NNODES|LOCALID|NODELIST|NPROCS|PROCID|TASKS_PER'
> hpmpi/node1.1.of.4
> > > SLURM_NODELIST=node[1-2]
> > > SLURM_TASKS_PER_NODE=2(x2)
> > > SLURM_STEP_NODELIST=node[1-2]
> > > SLURM_STEP_TASKS_PER_NODE=2(x2)
> > > SLURM_NNODES=2
> > > SLURM_NPROCS=4
> > > SLURM_NODEID=0
> > > SLURM_PROCID=1
> > > SLURM_LOCALID=1
> > > [brent_at_node2 mpi]$ egrep
> 'NODEID|NNODES|LOCALID|NODELIST|NPROCS|PROCID|TASKS_PER'
> hpmpi/node2.3.of.4
> > > SLURM_NODELIST=node[1-2]
> > > SLURM_TASKS_PER_NODE=2(x2)
> > > SLURM_STEP_NODELIST=node[1-2]
> > > SLURM_STEP_TASKS_PER_NODE=2(x2)
> > > SLURM_NNODES=2
> > > SLURM_NPROCS=4
> > > SLURM_NODEID=1
> > > SLURM_PROCID=3
> > > SLURM_LOCALID=1
> > > [brent_at_node2 mpi]$
> > >
> > > _______________________________________________
> > > users mailing list
> > > users_at_[hidden]
> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
> > >
> > > _______________________________________________
> > > users mailing list
> > > users_at_[hidden]
> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
> >
> > --
> > Jeff Squyres
> > jsquyres_at_[hidden]
> > For corporate legal information go to:
> > http://www.cisco.com/web/about/doing_business/legal/cri/
> >
> >
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquyres_at_[hidden]
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users