The usual cause of this problem is that the nodename in the machinefile is given as a00551, while Torque is assigning the node name as a00551.science.domain. Thus, mpirun thinks those are two separate nodes and winds up spawning an orted on its own node.
You might try ensuring that your machinefile is using the exact same name as provided in your allocation > On Sep 7, 2016, at 7:06 AM, Gilles Gouaillardet > <gilles.gouaillar...@gmail.com> wrote: > > Thanjs for the ligs > > From what i see now, it looks like a00551 is running both mpirun and orted, > though it should only run mpirun, and orted should run only on a00553 > > I will check the code and see what could be happening here > > Btw, what is the output of > hostname > hostname -f > On a00551 ? > > Out of curiosity, is a previous version of Open MPI (e.g. v1.10.4) installled > and running correctly on your cluster ? > > Cheers, > > Gilles > > Oswin Krause <oswin.kra...@ruhr-uni-bochum.de> wrote: >> Hi Gilles, >> >> Thanks for the hint with the machinefile. I know it is not equivalent >> and i do not intend to use that approach. I just wanted to know whether >> I could start the program successfully at all. >> >> Outside torque(4.2), rsh seems to be used which works fine, querying a >> password if no kerberos ticket is there >> >> Here is the output: >> [zbh251@a00551 ~]$ mpirun -V >> mpirun (Open MPI) 2.0.1 >> [zbh251@a00551 ~]$ ompi_info | grep ras >> MCA ras: loadleveler (MCA v2.1.0, API v2.0.0, Component >> v2.0.1) >> MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component >> v2.0.1) >> MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component >> v2.0.1) >> MCA ras: tm (MCA v2.1.0, API v2.0.0, Component v2.0.1) >> [zbh251@a00551 ~]$ mpirun --mca plm_base_verbose 10 --tag-output >> -display-map hostname >> [a00551.science.domain:04104] mca: base: components_register: >> registering framework plm components >> [a00551.science.domain:04104] mca: base: components_register: found >> loaded component isolated >> [a00551.science.domain:04104] mca: base: components_register: component >> isolated has no register or open function >> [a00551.science.domain:04104] mca: base: components_register: found >> loaded component rsh >> [a00551.science.domain:04104] mca: base: components_register: component >> rsh register function successful >> [a00551.science.domain:04104] mca: base: components_register: found >> loaded component slurm >> [a00551.science.domain:04104] mca: base: components_register: component >> slurm register function successful >> [a00551.science.domain:04104] mca: base: components_register: found >> loaded component tm >> [a00551.science.domain:04104] mca: base: components_register: component >> tm register function successful >> [a00551.science.domain:04104] mca: base: components_open: opening plm >> components >> [a00551.science.domain:04104] mca: base: components_open: found loaded >> component isolated >> [a00551.science.domain:04104] mca: base: components_open: component >> isolated open function successful >> [a00551.science.domain:04104] mca: base: components_open: found loaded >> component rsh >> [a00551.science.domain:04104] mca: base: components_open: component rsh >> open function successful >> [a00551.science.domain:04104] mca: base: components_open: found loaded >> component slurm >> [a00551.science.domain:04104] mca: base: components_open: component >> slurm open function successful >> [a00551.science.domain:04104] mca: base: components_open: found loaded >> component tm >> [a00551.science.domain:04104] mca: base: components_open: component tm >> open function successful >> [a00551.science.domain:04104] mca:base:select: Auto-selecting plm >> components >> [a00551.science.domain:04104] mca:base:select:( plm) Querying component >> [isolated] >> [a00551.science.domain:04104] mca:base:select:( plm) Query of component >> [isolated] set priority to 0 >> [a00551.science.domain:04104] mca:base:select:( plm) Querying component >> [rsh] >> [a00551.science.domain:04104] mca:base:select:( plm) Query of component >> [rsh] set priority to 10 >> [a00551.science.domain:04104] mca:base:select:( plm) Querying component >> [slurm] >> [a00551.science.domain:04104] mca:base:select:( plm) Querying component >> [tm] >> [a00551.science.domain:04104] mca:base:select:( plm) Query of component >> [tm] set priority to 75 >> [a00551.science.domain:04104] mca:base:select:( plm) Selected component >> [tm] >> [a00551.science.domain:04104] mca: base: close: component isolated >> closed >> [a00551.science.domain:04104] mca: base: close: unloading component >> isolated >> [a00551.science.domain:04104] mca: base: close: component rsh closed >> [a00551.science.domain:04104] mca: base: close: unloading component rsh >> [a00551.science.domain:04104] mca: base: close: component slurm closed >> [a00551.science.domain:04104] mca: base: close: unloading component >> slurm >> [a00551.science.domain:04109] mca: base: components_register: >> registering framework plm components >> [a00551.science.domain:04109] mca: base: components_register: found >> loaded component rsh >> [a00551.science.domain:04109] mca: base: components_register: component >> rsh register function successful >> [a00551.science.domain:04109] mca: base: components_open: opening plm >> components >> [a00551.science.domain:04109] mca: base: components_open: found loaded >> component rsh >> [a00551.science.domain:04109] mca: base: components_open: component rsh >> open function successful >> [a00551.science.domain:04109] mca:base:select: Auto-selecting plm >> components >> [a00551.science.domain:04109] mca:base:select:( plm) Querying component >> [rsh] >> [a00551.science.domain:04109] mca:base:select:( plm) Query of component >> [rsh] set priority to 10 >> [a00551.science.domain:04109] mca:base:select:( plm) Selected component >> [rsh] >> [a00551.science.domain:04109] [[53688,0],1] bind() failed on error >> Address already in use (98) >> [a00551.science.domain:04109] [[53688,0],1] ORTE_ERROR_LOG: Error in >> file oob_usock_component.c at line 228 >> Data for JOB [53688,1] offset 0 >> >> ======================== JOB MAP ======================== >> >> Data for node: a00551 Num slots: 2 Max slots: 0 Num procs: 2 >> Process OMPI jobid: [53688,1] App: 0 Process rank: 0 Bound: socket >> 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt >> 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket >> 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt >> 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt >> 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] >> Process OMPI jobid: [53688,1] App: 0 Process rank: 1 Bound: socket >> 1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt >> 0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket >> 1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt >> 0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt >> 0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB] >> >> Data for node: a00553.science.domain Num slots: 1 Max slots: 0 Num >> procs: 1 >> Process OMPI jobid: [53688,1] App: 0 Process rank: 2 Bound: socket >> 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt >> 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket >> 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt >> 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt >> 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] >> >> ============================================================= >> [a00551.science.domain:04104] [[53688,0],0] complete_setup on job >> [53688,1] >> [a00551.science.domain:04104] [[53688,0],0] plm:base:receive update proc >> state command from [[53688,0],1] >> [a00551.science.domain:04104] [[53688,0],0] plm:base:receive got >> update_proc_state for job [53688,1] >> [1,0]<stdout>:a00551.science.domain >> [1,2]<stdout>:a00551.science.domain >> [a00551.science.domain:04104] [[53688,0],0] plm:base:receive update proc >> state command from [[53688,0],1] >> [a00551.science.domain:04104] [[53688,0],0] plm:base:receive got >> update_proc_state for job [53688,1] >> [1,1]<stdout>:a00551.science.domain >> [a00551.science.domain:04109] mca: base: close: component rsh closed >> [a00551.science.domain:04109] mca: base: close: unloading component rsh >> [a00551.science.domain:04104] mca: base: close: component tm closed >> [a00551.science.domain:04104] mca: base: close: unloading component tm >> >> On 2016-09-07 14:41, Gilles Gouaillardet wrote: >>> Hi, >>> >>> Which version of Open MPI are you running ? >>> >>> I noted that though you are asking three nodes and one task per node, >>> you have been allocated 2 nodes only. >>> I do not know if this is related to this issue. >>> >>> Note if you use the machinefile, a00551 has two slots (since it >>> appears twice in the machinefile) but a00553 has 20 slots (since it >>> appears once in the machinefile, the number of slots is automatically >>> detected) >>> >>> Can you run >>> mpirun --mca plm_base_verbose 10 ... >>> So we can confirm tm is used. >>> >>> Before invoking mpirun, you might want to cleanup the ompi directory in >>> /tmp >>> >>> Cheers, >>> >>> Gilles >>> >>> Oswin Krause <oswin.kra...@ruhr-uni-bochum.de> wrote: >>>> Hi, >>>> >>>> I am currently trying to set up OpenMPI in torque. OpenMPI is build >>>> with >>>> tm support. Torque is correctly assigning nodes and I can run >>>> mpi-programs on single nodes just fine. the problem starts when >>>> processes are split between nodes. >>>> >>>> For example, I create an interactive session with torque and start a >>>> program by >>>> >>>> qsub -I -n -l nodes=3:ppn=1 >>>> mpirun --tag-output -display-map hostname >>>> >>>> which leads to >>>> [a00551.science.domain:15932] [[65415,0],1] bind() failed on error >>>> Address already in use (98) >>>> [a00551.science.domain:15932] [[65415,0],1] ORTE_ERROR_LOG: Error in >>>> file oob_usock_component.c at line 228 >>>> Data for JOB [65415,1] offset 0 >>>> >>>> ======================== JOB MAP ======================== >>>> >>>> Data for node: a00551 Num slots: 2 Max slots: 0 Num procs: 2 >>>> Process OMPI jobid: [65415,1] App: 0 Process rank: 0 Bound: socket >>>> 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt >>>> 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket >>>> 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt >>>> 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt >>>> 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] >>>> Process OMPI jobid: [65415,1] App: 0 Process rank: 1 Bound: socket >>>> 1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt >>>> 0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket >>>> 1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt >>>> 0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt >>>> 0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB] >>>> >>>> Data for node: a00553.science.domain Num slots: 1 Max slots: 0 >>>> Num >>>> procs: 1 >>>> Process OMPI jobid: [65415,1] App: 0 Process rank: 2 Bound: socket >>>> 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt >>>> 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket >>>> 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt >>>> 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt >>>> 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] >>>> >>>> ============================================================= >>>> [1,0]<stdout>:a00551.science.domain >>>> [1,2]<stdout>:a00551.science.domain >>>> [1,1]<stdout>:a00551.science.domain >>>> >>>> >>>> if I login on a00551 and start using the hostfile generated by the >>>> PBS_NODEFILE, everything works: >>>> >>>> (from within the interactive session) >>>> echo $PBS_NODEFILE >>>> /var/lib/torque/aux//278.a00552.science.domain >>>> cat $PBS_NODEFILE >>>> a00551.science.domain >>>> a00553.science.domain >>>> a00551.science.domain >>>> >>>> (from within the separate login) >>>> mpirun --hostfile /var/lib/torque/aux//278.a00552.science.domain -np 3 >>>> --tag-output -display-map hostname >>>> >>>> Data for JOB [65445,1] offset 0 >>>> >>>> ======================== JOB MAP ======================== >>>> >>>> Data for node: a00551 Num slots: 2 Max slots: 0 Num procs: 2 >>>> Process OMPI jobid: [65445,1] App: 0 Process rank: 0 Bound: socket >>>> 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt >>>> 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket >>>> 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt >>>> 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt >>>> 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] >>>> Process OMPI jobid: [65445,1] App: 0 Process rank: 1 Bound: socket >>>> 1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt >>>> 0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket >>>> 1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt >>>> 0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt >>>> 0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB] >>>> >>>> Data for node: a00553.science.domain Num slots: 20 Max slots: 0 >>>> Num >>>> procs: 1 >>>> Process OMPI jobid: [65445,1] App: 0 Process rank: 2 Bound: socket >>>> 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt >>>> 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket >>>> 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt >>>> 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt >>>> 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] >>>> >>>> ============================================================= >>>> [1,0]<stdout>:a00551.science.domain >>>> [1,2]<stdout>:a00553.science.domain >>>> [1,1]<stdout>:a00551.science.domain >>>> >>>> I am kind of lost whats going on here. Anyone having an idea? I am >>>> seriously considering this to be the problem of kerberos >>>> authentification that we have to work with, but I fail to see how this >>>> should affect the sockets. >>>> >>>> Best, >>>> Oswin >>>> _______________________________________________ >>>> users mailing list >>>> users@lists.open-mpi.org >>>> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >>> _______________________________________________ >>> users mailing list >>> users@lists.open-mpi.org >>> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://rfd.newmexicoconsortium.org/mailman/listinfo/users _______________________________________________ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users
