Sorry Ralph, I have to respectfully disagree with you on this one. I believe that the output below shows that the issue is that the two different MPIs launch things differently. On one node, I ran:
[brent@node2 mpi]$ which mpirun ~/bin/openmpi143/bin/mpirun [brent@node2 mpi]$ mpirun -np 4 --bynode sleep 300 And then checked the process tree on the remote node: [brent@node1 mpi]$ ps -fu brent UID PID PPID C STIME TTY TIME CMD brent 1709 1706 0 10:00 ? 00:00:00 /mnt/node1/home/brent/bin/openmpi143/bin/orted -mca brent 1712 1709 0 10:00 ? 00:00:00 sleep 300 brent 1713 1709 0 10:00 ? 00:00:00 sleep 300 brent 1714 18458 0 10:00 pts/0 00:00:00 ps -fu brent brent 13282 13281 0 Feb17 pts/0 00:00:00 -bash brent 18458 13282 0 Feb23 pts/0 00:00:00 -csh [brent@node1 mpi]$ ps -fp 1706 UID PID PPID C STIME TTY TIME CMD root 1706 1 0 10:00 ? 00:00:00 slurmstepd: [29.9] [brent@node1 mpi]$ Note that the parent of the sleep processes is orted and that orted was started by slurmstepd. Unless orted is updating the slurm variables for the children (which is doubtful) then they will not contain the specific settings that I see when I run srun directly. I launch with HP-MPI like this: [brent@node2 mpi]$ /opt/hpmpi/bin/mpirun -srun -N 2 -n 4 sleep 300 I then see the following in the process tree on the remote node: [brent@node1 mpi]$ ps -fu brent UID PID PPID C STIME TTY TIME CMD brent 1741 1738 0 10:02 ? 00:00:00 /bin/sleep 300 brent 1742 1738 0 10:02 ? 00:00:00 /bin/sleep 300 brent 1745 18458 0 10:02 pts/0 00:00:00 ps -fu brent brent 13282 13281 0 Feb17 pts/0 00:00:00 -bash brent 18458 13282 0 Feb23 pts/0 00:00:00 -csh [brent@node1 mpi]$ ps -fp 1738 UID PID PPID C STIME TTY TIME CMD root 1738 1 0 10:02 ? 00:00:00 slurmstepd: [29.10] [brent@node1 mpi]$ Since the parent of both of the sleep processes is slurmstepd, it is setting things up as I would expect. This lineage is the same as I find by running srun directly. Now, the question still is, why does this work for Jeff? :) Is there a way to get orted out of the way so the sleep processes are launched directly by srun? brent From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Ralph Castain Sent: Thursday, February 24, 2011 10:05 AM To: Open MPI Users Subject: Re: [OMPI users] SLURM environment variables at runtime I would talk to the slurm folks about it - I don't know anything about the internals of HP-MPI, but I do know the relevant OMPI internals. OMPI doesn't do anything with respect to the envars. We just use "srun -hostlist <fff>" to launch the daemons. Each daemon subsequently gets a message telling it what local procs to run, and then fork/exec's those procs. The environment set for those procs is a copy of that given to the daemon, including any and all slurm values. So whatever slurm sets, your procs get. My guess is that HP-MPI is doing something with the envars to create the difference. As for running OMPI procs directly from srun: the slurm folks put out a faq (or its equivalent) on it, I believe. I don't recall the details (even though I wrote the integration...). If you google our user and/or devel mailing lists, though, you'll see threads discussing it. Look for "slurmd" in the text - that's the ORTE integration module for that feature. On Thu, Feb 24, 2011 at 8:55 AM, Henderson, Brent <brent.hender...@hp.com> wrote: 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@node2 mpi]$ salloc -N 2 salloc: Granted job allocation 29 [brent@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@node2 mpi]$ srun env | egrep ^SLURM_ | wc -l 66 [brent@node2 mpi]$ srun env | egrep ^SLURM_ | sort > srun.out [brent@node2 mpi]$ which mpirun ~/bin/openmpi143/bin/mpirun [brent@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@node2 mpi]$ which mpirun ~/bin/openmpi143/bin/mpirun [brent@node2 mpi]$ mpirun -np 2 --bynode env | egrep ^SLURM_ | wc -l 42 <-- note, not 66 as above! [brent@node2 mpi]$ mpirun -np 2 --bynode env | egrep ^SLURM_ | sort > mpirun.out [brent@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@node2 mpi]$ [brent@node2 mpi]$ [brent@node2 mpi]$ [brent@node2 mpi]$ [brent@node2 mpi]$ /opt/hpmpi/bin/mpirun -srun -n 2 -N 2 env | egrep ^SLURM_ | sort > hpmpi.out [brent@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@node2 mpi]$ [brent@node2 mpi]$ [brent@node2 mpi]$ grep SLURM_PROCID srun.out SLURM_PROCID=0 SLURM_PROCID=1 [brent@node2 mpi]$ grep SLURM_PROCID mpirun.out SLURM_PROCID=0 [brent@node2 mpi]$ grep SLURM_PROCID hpmpi.out SLURM_PROCID=0 SLURM_PROCID=1 [brent@node2 mpi]$ > -----Original Message----- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] 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 <jsquy...@cisco.com> > 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@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@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-boun...@open-mpi.org [mailto:users-bounces@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.hender...@hp.com> 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@node2 mpi]$ rm node* > > > [brent@node2 mpi]$ mkdir openmpi hpmpi > > > [brent@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@node2 mpi]$ mv node* openmpi/ > > > [brent@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@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@node2 mpi]$ > > > > > > > > > [brent@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@node2 mpi]$ mv node* hpmpi/ > > > [brent@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@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@node2 mpi]$ > > > > > > _______________________________________________ > > > users mailing list > > > us...@open-mpi.org > > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > _______________________________________________ > > > users mailing list > > > us...@open-mpi.org > > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > -- > > Jeff Squyres > > jsquy...@cisco.com > > For corporate legal information go to: > > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > > > > _______________________________________________ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > _______________________________________________ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users _______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
