Re: [OMPI users] debugs for jobs not starting
Something doesn't make sense here. If you direct launch with srun, there is no orted involved. The orted only gets launched if you start with mpirun Did you configure --with-pmi and point to where that include file resides? Otherwise, the procs will all think they are singletons Sent from my iPhone On Oct 12, 2012, at 7:27 AM, Michael Di Domenico wrote: > what isn't working is when i fire off an MPI job with over 800 ranks, > they don't all actually start up a process > > fe, if i do srun -n 1024 --ntasks-per-node 12 xhpl > > and then do a 'pgrep xhpl | wc -l', on all of the allocated nodes, not > all of them have actually started xhpl > > most will read 12 started processes, but an inconsistent list of nodes > will fail to actually start xhpl and stall the whole job > > if i look at all the nodes allocated to my job, it does start the orte > process though > > what i need to figure out, is why the orte process starts, but fails > to actually start xhpl on some of the nodes > > unfortunately, the list of nodes that don't start xhpl during my runs > changes each time and no hardware errors are being detected. if i > cancel the job and restart the job over and over, eventually one will > actually kick off and run to completion. > > if i run the process outside of slurm just using openmpi, it seems to > behave correctly, so i'm leaning towards a slurm interacting with > openmpi problem. > > what i'd like to do is instrument a debug in openmpi that will tell me > what openmpi is waiting on in order to kick off the xhpl binary > > i'm testing to see whether it's a psm related problem now, i'll check > back if i can narrow the scope a little more > > On Thu, Oct 11, 2012 at 10:21 PM, Ralph Castain wrote: >> I'm afraid I'm confused - I don't understand what is and isn't working. What >> "next process" isn't starting? >> >> >> On Thu, Oct 11, 2012 at 9:41 AM, Michael Di Domenico >> wrote: >>> >>> adding some additional info >>> >>> did an strace on an orted process where xhpl failed to start, i did >>> this after the mpirun execution, so i probably missed some output, but >>> it keeps scrolling >>> >>> poll([{fd=4, events=POLLIN},{fd=7, events=POLLIN},{fd=8, >>> events=POLLIN},{fd=10, events=POLLIN},{fd=12, events=POLLIN},{fd=13, >>> events=POLLIN},{fd=14, events=POLLIN},{fd=15, events=POLLIN},{fd=16, >>> events=POLLIN}], 9, 1000) = 0 (Timeout) >>> >>> i didn't see anything useful in /proc under those file descriptors, >>> but perhaps i missed something i don't know to look for >>> >>> On Thu, Oct 11, 2012 at 12:06 PM, Michael Di Domenico >>> wrote: too add a little more detail, it looks like xhpl is not actually starting on all nodes when i kick off the mpirun each time i cancel and restart the job, the nodes that do not start change, so i can't call it a bad node if i disable infiniband with --mca btl self,sm,tcp on occasion i can get xhpl to actually run, but it's not consistent i'm going to check my ethernet network and make sure there's no problems there (could this be an OOB error with mpirun?), on the nodes that fail to start xhpl, i do see the orte process, but nothing in the logs about why it failed to launch xhpl On Thu, Oct 11, 2012 at 11:49 AM, Michael Di Domenico wrote: > I'm trying to diagnose an MPI job (in this case xhpl), that fails to > start when the rank count gets fairly high into the thousands. > > My symptom is the jobs fires up via slurm, and I can see all the xhpl > processes on the nodes, but it never kicks over to the next process. > > My question is, what debugs should I turn on to tell me what the > system might be waiting on? > > I've checked a bunch of things, but I'm probably overlooking something > trivial (which is par for me). > > I'm using the Openmpi 1.6.1, Slurm 2.4.2 on CentOS 6.3, with > Infiniband/PSM >>> ___ >>> 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 > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] debugs for jobs not starting
Hi I don't use Slurm, and our clusters are fairly small (few tens of nodes, few hundred cores). Having said that, I know that Torque, which we use here, requires specific system configuration changes on large clusters, like increasing the maximum number of open files, increasing the ARP cache size, etc. Apparently Slrum also needs some system tweaking on large clusters: https://computing.llnl.gov/linux/slurm/big_sys.html Could this be the problem? Anyway, just a thought. Gus Correa On 10/12/2012 09:27 AM, Michael Di Domenico wrote: what isn't working is when i fire off an MPI job with over 800 ranks, they don't all actually start up a process fe, if i do srun -n 1024 --ntasks-per-node 12 xhpl and then do a 'pgrep xhpl | wc -l', on all of the allocated nodes, not all of them have actually started xhpl most will read 12 started processes, but an inconsistent list of nodes will fail to actually start xhpl and stall the whole job if i look at all the nodes allocated to my job, it does start the orte process though what i need to figure out, is why the orte process starts, but fails to actually start xhpl on some of the nodes unfortunately, the list of nodes that don't start xhpl during my runs changes each time and no hardware errors are being detected. if i cancel the job and restart the job over and over, eventually one will actually kick off and run to completion. if i run the process outside of slurm just using openmpi, it seems to behave correctly, so i'm leaning towards a slurm interacting with openmpi problem. what i'd like to do is instrument a debug in openmpi that will tell me what openmpi is waiting on in order to kick off the xhpl binary i'm testing to see whether it's a psm related problem now, i'll check back if i can narrow the scope a little more On Thu, Oct 11, 2012 at 10:21 PM, Ralph Castain wrote: I'm afraid I'm confused - I don't understand what is and isn't working. What "next process" isn't starting? On Thu, Oct 11, 2012 at 9:41 AM, Michael Di Domenico wrote: adding some additional info did an strace on an orted process where xhpl failed to start, i did this after the mpirun execution, so i probably missed some output, but it keeps scrolling poll([{fd=4, events=POLLIN},{fd=7, events=POLLIN},{fd=8, events=POLLIN},{fd=10, events=POLLIN},{fd=12, events=POLLIN},{fd=13, events=POLLIN},{fd=14, events=POLLIN},{fd=15, events=POLLIN},{fd=16, events=POLLIN}], 9, 1000) = 0 (Timeout) i didn't see anything useful in /proc under those file descriptors, but perhaps i missed something i don't know to look for On Thu, Oct 11, 2012 at 12:06 PM, Michael Di Domenico wrote: too add a little more detail, it looks like xhpl is not actually starting on all nodes when i kick off the mpirun each time i cancel and restart the job, the nodes that do not start change, so i can't call it a bad node if i disable infiniband with --mca btl self,sm,tcp on occasion i can get xhpl to actually run, but it's not consistent i'm going to check my ethernet network and make sure there's no problems there (could this be an OOB error with mpirun?), on the nodes that fail to start xhpl, i do see the orte process, but nothing in the logs about why it failed to launch xhpl On Thu, Oct 11, 2012 at 11:49 AM, Michael Di Domenico wrote: I'm trying to diagnose an MPI job (in this case xhpl), that fails to start when the rank count gets fairly high into the thousands. My symptom is the jobs fires up via slurm, and I can see all the xhpl processes on the nodes, but it never kicks over to the next process. My question is, what debugs should I turn on to tell me what the system might be waiting on? I've checked a bunch of things, but I'm probably overlooking something trivial (which is par for me). I'm using the Openmpi 1.6.1, Slurm 2.4.2 on CentOS 6.3, with Infiniband/PSM ___ 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 ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] debugs for jobs not starting
turned on the daemon debugs for orted and noticed this difference i get this on all the good nodes (ones that actually started xhpl) Daemon was launched on node08 - beginning to initialize [node08:21230] [[64354,0],1] orted_cmd: received add_local_procs [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],84] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],85] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],86] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],87] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],88] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],89] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],90] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],91] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],92] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],93] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],94] [node08:21230] [[64354,0],0] orted_recv: received sync+nidmap from local proc [[64354,1],95] [node08:21230] [[64354,0],1] orted: up and running - waiting for commands! [node08:21230] procdir: /tmp/openmpi-sessions-user@node08_0/28/1/1 [node08:21230] jobdir: /tmp/openmpi-sessions-user@node08_/44228/1 [node08:21230] top: openmpi-sessions-user@node08_0 [node08:21230] tmp: /tmp [...repeats the above five lines a bunch of times...] --- get this on the ones that do not start xhpl Daemon was launched on node06 - beginning to initialize [node06:11230] [[46344,0],1] orted: up and running - waiting for commands! [node06:11230] procdir: /tmp/openmpi-sessions-user@node06_0/28/1/1 [node06:11230] jobdir: /tmp/openmpi-sessions-user@node06_/44228/1 [node06:11230] top: openmpi-sessions-user@node06_0 [node06:11230] tmp: /tmp [...above lines only come out once...] On Fri, Oct 12, 2012 at 9:27 AM, Michael Di Domenico wrote: > what isn't working is when i fire off an MPI job with over 800 ranks, > they don't all actually start up a process > > fe, if i do srun -n 1024 --ntasks-per-node 12 xhpl > > and then do a 'pgrep xhpl | wc -l', on all of the allocated nodes, not > all of them have actually started xhpl > > most will read 12 started processes, but an inconsistent list of nodes > will fail to actually start xhpl and stall the whole job > > if i look at all the nodes allocated to my job, it does start the orte > process though > > what i need to figure out, is why the orte process starts, but fails > to actually start xhpl on some of the nodes > > unfortunately, the list of nodes that don't start xhpl during my runs > changes each time and no hardware errors are being detected. if i > cancel the job and restart the job over and over, eventually one will > actually kick off and run to completion. > > if i run the process outside of slurm just using openmpi, it seems to > behave correctly, so i'm leaning towards a slurm interacting with > openmpi problem. > > what i'd like to do is instrument a debug in openmpi that will tell me > what openmpi is waiting on in order to kick off the xhpl binary > > i'm testing to see whether it's a psm related problem now, i'll check > back if i can narrow the scope a little more > > On Thu, Oct 11, 2012 at 10:21 PM, Ralph Castain wrote: >> I'm afraid I'm confused - I don't understand what is and isn't working. What >> "next process" isn't starting? >> >> >> On Thu, Oct 11, 2012 at 9:41 AM, Michael Di Domenico >> wrote: >>> >>> adding some additional info >>> >>> did an strace on an orted process where xhpl failed to start, i did >>> this after the mpirun execution, so i probably missed some output, but >>> it keeps scrolling >>> >>> poll([{fd=4, events=POLLIN},{fd=7, events=POLLIN},{fd=8, >>> events=POLLIN},{fd=10, events=POLLIN},{fd=12, events=POLLIN},{fd=13, >>> events=POLLIN},{fd=14, events=POLLIN},{fd=15, events=POLLIN},{fd=16, >>> events=POLLIN}], 9, 1000) = 0 (Timeout) >>> >>> i didn't see anything useful in /proc under those file descriptors, >>> but perhaps i missed something i don't know to look for >>> >>> On Thu, Oct 11, 2012 at 12:06 PM, Michael Di Domenico >>> wrote: >>> > too add a little more detail, it looks like xhpl is not actually >>> > starting on all nodes when i kick off the mpirun >>> > >>> > each time i cancel and restart the job, the nodes that do not start >>> > change, so i can't call it a bad node >>> > >>> > if i disable infiniband with --mca btl self,sm,tcp on occasion i can >>> > get xhpl to actually run, but it's not consistent >>> > >>> > i'm going to check my ethernet network and make sure there's no >>> > problems there (could this be an OOB error with mpirun?), on the nodes >>> > that fail t
Re: [OMPI users] debugs for jobs not starting
what isn't working is when i fire off an MPI job with over 800 ranks, they don't all actually start up a process fe, if i do srun -n 1024 --ntasks-per-node 12 xhpl and then do a 'pgrep xhpl | wc -l', on all of the allocated nodes, not all of them have actually started xhpl most will read 12 started processes, but an inconsistent list of nodes will fail to actually start xhpl and stall the whole job if i look at all the nodes allocated to my job, it does start the orte process though what i need to figure out, is why the orte process starts, but fails to actually start xhpl on some of the nodes unfortunately, the list of nodes that don't start xhpl during my runs changes each time and no hardware errors are being detected. if i cancel the job and restart the job over and over, eventually one will actually kick off and run to completion. if i run the process outside of slurm just using openmpi, it seems to behave correctly, so i'm leaning towards a slurm interacting with openmpi problem. what i'd like to do is instrument a debug in openmpi that will tell me what openmpi is waiting on in order to kick off the xhpl binary i'm testing to see whether it's a psm related problem now, i'll check back if i can narrow the scope a little more On Thu, Oct 11, 2012 at 10:21 PM, Ralph Castain wrote: > I'm afraid I'm confused - I don't understand what is and isn't working. What > "next process" isn't starting? > > > On Thu, Oct 11, 2012 at 9:41 AM, Michael Di Domenico > wrote: >> >> adding some additional info >> >> did an strace on an orted process where xhpl failed to start, i did >> this after the mpirun execution, so i probably missed some output, but >> it keeps scrolling >> >> poll([{fd=4, events=POLLIN},{fd=7, events=POLLIN},{fd=8, >> events=POLLIN},{fd=10, events=POLLIN},{fd=12, events=POLLIN},{fd=13, >> events=POLLIN},{fd=14, events=POLLIN},{fd=15, events=POLLIN},{fd=16, >> events=POLLIN}], 9, 1000) = 0 (Timeout) >> >> i didn't see anything useful in /proc under those file descriptors, >> but perhaps i missed something i don't know to look for >> >> On Thu, Oct 11, 2012 at 12:06 PM, Michael Di Domenico >> wrote: >> > too add a little more detail, it looks like xhpl is not actually >> > starting on all nodes when i kick off the mpirun >> > >> > each time i cancel and restart the job, the nodes that do not start >> > change, so i can't call it a bad node >> > >> > if i disable infiniband with --mca btl self,sm,tcp on occasion i can >> > get xhpl to actually run, but it's not consistent >> > >> > i'm going to check my ethernet network and make sure there's no >> > problems there (could this be an OOB error with mpirun?), on the nodes >> > that fail to start xhpl, i do see the orte process, but nothing in the >> > logs about why it failed to launch xhpl >> > >> > >> > >> > On Thu, Oct 11, 2012 at 11:49 AM, Michael Di Domenico >> > wrote: >> >> I'm trying to diagnose an MPI job (in this case xhpl), that fails to >> >> start when the rank count gets fairly high into the thousands. >> >> >> >> My symptom is the jobs fires up via slurm, and I can see all the xhpl >> >> processes on the nodes, but it never kicks over to the next process. >> >> >> >> My question is, what debugs should I turn on to tell me what the >> >> system might be waiting on? >> >> >> >> I've checked a bunch of things, but I'm probably overlooking something >> >> trivial (which is par for me). >> >> >> >> I'm using the Openmpi 1.6.1, Slurm 2.4.2 on CentOS 6.3, with >> >> Infiniband/PSM >> ___ >> 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
Re: [OMPI users] debugs for jobs not starting
I'm afraid I'm confused - I don't understand what is and isn't working. What "next process" isn't starting? On Thu, Oct 11, 2012 at 9:41 AM, Michael Di Domenico wrote: > adding some additional info > > did an strace on an orted process where xhpl failed to start, i did > this after the mpirun execution, so i probably missed some output, but > it keeps scrolling > > poll([{fd=4, events=POLLIN},{fd=7, events=POLLIN},{fd=8, > events=POLLIN},{fd=10, events=POLLIN},{fd=12, events=POLLIN},{fd=13, > events=POLLIN},{fd=14, events=POLLIN},{fd=15, events=POLLIN},{fd=16, > events=POLLIN}], 9, 1000) = 0 (Timeout) > > i didn't see anything useful in /proc under those file descriptors, > but perhaps i missed something i don't know to look for > > On Thu, Oct 11, 2012 at 12:06 PM, Michael Di Domenico > wrote: > > too add a little more detail, it looks like xhpl is not actually > > starting on all nodes when i kick off the mpirun > > > > each time i cancel and restart the job, the nodes that do not start > > change, so i can't call it a bad node > > > > if i disable infiniband with --mca btl self,sm,tcp on occasion i can > > get xhpl to actually run, but it's not consistent > > > > i'm going to check my ethernet network and make sure there's no > > problems there (could this be an OOB error with mpirun?), on the nodes > > that fail to start xhpl, i do see the orte process, but nothing in the > > logs about why it failed to launch xhpl > > > > > > > > On Thu, Oct 11, 2012 at 11:49 AM, Michael Di Domenico > > wrote: > >> I'm trying to diagnose an MPI job (in this case xhpl), that fails to > >> start when the rank count gets fairly high into the thousands. > >> > >> My symptom is the jobs fires up via slurm, and I can see all the xhpl > >> processes on the nodes, but it never kicks over to the next process. > >> > >> My question is, what debugs should I turn on to tell me what the > >> system might be waiting on? > >> > >> I've checked a bunch of things, but I'm probably overlooking something > >> trivial (which is par for me). > >> > >> I'm using the Openmpi 1.6.1, Slurm 2.4.2 on CentOS 6.3, with > Infiniband/PSM > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
Re: [OMPI users] debugs for jobs not starting
adding some additional info did an strace on an orted process where xhpl failed to start, i did this after the mpirun execution, so i probably missed some output, but it keeps scrolling poll([{fd=4, events=POLLIN},{fd=7, events=POLLIN},{fd=8, events=POLLIN},{fd=10, events=POLLIN},{fd=12, events=POLLIN},{fd=13, events=POLLIN},{fd=14, events=POLLIN},{fd=15, events=POLLIN},{fd=16, events=POLLIN}], 9, 1000) = 0 (Timeout) i didn't see anything useful in /proc under those file descriptors, but perhaps i missed something i don't know to look for On Thu, Oct 11, 2012 at 12:06 PM, Michael Di Domenico wrote: > too add a little more detail, it looks like xhpl is not actually > starting on all nodes when i kick off the mpirun > > each time i cancel and restart the job, the nodes that do not start > change, so i can't call it a bad node > > if i disable infiniband with --mca btl self,sm,tcp on occasion i can > get xhpl to actually run, but it's not consistent > > i'm going to check my ethernet network and make sure there's no > problems there (could this be an OOB error with mpirun?), on the nodes > that fail to start xhpl, i do see the orte process, but nothing in the > logs about why it failed to launch xhpl > > > > On Thu, Oct 11, 2012 at 11:49 AM, Michael Di Domenico > wrote: >> I'm trying to diagnose an MPI job (in this case xhpl), that fails to >> start when the rank count gets fairly high into the thousands. >> >> My symptom is the jobs fires up via slurm, and I can see all the xhpl >> processes on the nodes, but it never kicks over to the next process. >> >> My question is, what debugs should I turn on to tell me what the >> system might be waiting on? >> >> I've checked a bunch of things, but I'm probably overlooking something >> trivial (which is par for me). >> >> I'm using the Openmpi 1.6.1, Slurm 2.4.2 on CentOS 6.3, with Infiniband/PSM
Re: [OMPI users] debugs for jobs not starting
too add a little more detail, it looks like xhpl is not actually starting on all nodes when i kick off the mpirun each time i cancel and restart the job, the nodes that do not start change, so i can't call it a bad node if i disable infiniband with --mca btl self,sm,tcp on occasion i can get xhpl to actually run, but it's not consistent i'm going to check my ethernet network and make sure there's no problems there (could this be an OOB error with mpirun?), on the nodes that fail to start xhpl, i do see the orte process, but nothing in the logs about why it failed to launch xhpl On Thu, Oct 11, 2012 at 11:49 AM, Michael Di Domenico wrote: > I'm trying to diagnose an MPI job (in this case xhpl), that fails to > start when the rank count gets fairly high into the thousands. > > My symptom is the jobs fires up via slurm, and I can see all the xhpl > processes on the nodes, but it never kicks over to the next process. > > My question is, what debugs should I turn on to tell me what the > system might be waiting on? > > I've checked a bunch of things, but I'm probably overlooking something > trivial (which is par for me). > > I'm using the Openmpi 1.6.1, Slurm 2.4.2 on CentOS 6.3, with Infiniband/PSM
[OMPI users] debugs for jobs not starting
I'm trying to diagnose an MPI job (in this case xhpl), that fails to start when the rank count gets fairly high into the thousands. My symptom is the jobs fires up via slurm, and I can see all the xhpl processes on the nodes, but it never kicks over to the next process. My question is, what debugs should I turn on to tell me what the system might be waiting on? I've checked a bunch of things, but I'm probably overlooking something trivial (which is par for me). I'm using the Openmpi 1.6.1, Slurm 2.4.2 on CentOS 6.3, with Infiniband/PSM